Rice is a very important food crop, which serves as staple food for more than half of the world's population. Furthermore, detailed genetic mapping and physical mapping of the rice genome is complete. Creating transgenic rice has become routine. Additionally, rice has colinearity with the genomes of other gramineous crops, therefore it has been viewed as a model plant. Therefore, the study of rice functional genes has significant meanings for social economic development and biological research.
The lack of adequate food supply is a challenge faced by the entire world. Rice yield has been dramatically increased by the two technology revolutions of dwarf rice plant of the 1950s and 1960s, and the hybrid rice of the 1970s. However, rice crops are still harmed by pests over large areas and rice production remains threatened, particularly by brown planthopper. Brown planthopper adults and nympha stab and suck the rice sap with their stylets, causing the leaves to turn yellow or to wither to death, which results in reduction or total destruction of the yield. According to China agriculture yearbook, there were severe outbreaks of brown planthopper nation wide in the years 1966, 1969, 1973, 1977, 1983 and 2003 and extremely severe outbreaks in the years 1987, 1991, 2005, 2006 and 2007. The harmed area accounts for more than 50% of the total rice cultivation and it caused a great loss to the rice production of China. Since the harm caused by brown planthopper occurs mainly during rice grain filling and ripening stages, large amounts of pesticide must be applied during this period, which risks contaminating the rice. There remains a need in the industry for a safer way to ensure a high yield from rice cultivation.
Using a brown planthopper resistance gene to breed pest resistance into a rice variety is the most economic and effective method for the integrated control of brown planthopper. The research results of International Rice Research Institute (IRRI) and the practical experience of rice production in Southeast Asia have shown that even rice varieties having medium level resistance are sufficient to control the brown planthopper population so as to have no discernable damage and that no actual harm and loss of yield are caused. Thus, isolating a brown planthopper resistance gene and applying it in the project of rice breeding are the fundamental measures for controlling damage in rice crops caused by brown planthopper.
The study of rice brown planthopper resistance gene began in the 1970s. Up to now, 19 major pest resistance genes have been named (for detailed reviews see Yang H Y et al., 2004 High-resolution genetic mapping at the Bph15 locus for brown planthopper resistance in rice. Theor Appl Genet. 110: 182-191). Among them, the resistance of the three rice varieties (Mudgo, CO22 and MTU15) is controlled by a single dominant gene, this gene is named as Bph1, and another recessive gene bph2, closely linked with Bph1, controls the resistance of rice variety ASD7. In their genetic study of 28 varieties, Lakshminarayana and Khush found that rice variety Rathu Heenati carries a dominant brown planthopper resistance gene Bph3, which is inherited independently from BPh1. In addition, rice variety Babawee contains a recessive gene bph4, which is also inherited independently from bph2. Sidhu and Khush found that Bph3 and bph4 are closely linked, bph4 is also linked with the semidwarf gene sd-1. The genetic analysis of Khush et al about rice variety ARC10550 showed that it contains the recessive gene bph5. In their study of 17 materials resistant to bio-type 4 BPH but sensitive to the other three bio-types, Kabir and Khush found that varieties Swarnalata and T12 contain one pest resistance gene respectively, which are named Bph6 and bph7. The discovery of bph8 and Bph9 is similar to that of the other genes, the recessive gene bph8 is not allelic to bph2 and bph4, the dominant gene. Bph9 is not allelic to Bph3 and Bph4. Among the afore-mentioned brown planthopper resistance genes, bph5, Bph6 and bph7 are resistant to brown planthopper bio-type 4, while exhibiting sensitivity to bio-types 1, 2 and 3.
Wild rice is also a source of brown planthopper resistance genes. In 1994, Ishii et al. identified a new dominant brown planthopper resistance gene Bph10 from a transformed line of Australian wild rice (O. australiensis), IR65482-4-136-2-2. This gene is resistant to brown planthopper bio-types 1, 2 and 3. Bph11 is identified from O. eichinger. Rice with a brown planthopper resistance gene can inhibit food fetching, growth and development, and reproduction of brown planthopper, so that the aim of pest resistance is achieved (Hao P Y et al., 2008 Herbivore-induced callose deposition on the sieve plates of rice: an important mechanism for host resistance. Plant Physiology 146: 1810-1820). However, up to now, no rice brown planthopper resistance gene has been cloned.
Map-based cloning is also called positional cloning, which is a gene cloning technology developed along with the development of molecular marker genetic linkage map. The steps of map-based cloning comprise genetic mapping of the target gene, physical mapping, sequence analysis and genetic transformation and test of function. Theoretically, any gene that is able to be positioned can be isolated by map-based cloning. Generally, map-based cloning is suitable for species with relatively small genomes, such as the monocot model plant rice, in which the ratio between genome physical distance and genetic distance is small and has plenty of markers. As a gramineous model plant, rice has a genome that is the center of a concentric circle formed by the genomes of 7 gramineous plants, such as wheat and broomcorn, and it is one of the crops most suitable to use map-based cloning to isolate a target gene. Multiple genes already cloned in rice were cloned by map-based cloning, for example, the Xanthomonas oryzae pv. oryzae resistance gene Xa-21 (Song W Y et al. 1995, A Receptor Kinase-Like Protein Encoded by the Rice Disease Resistance Gene, Xa21. Science, 270: 1804-1806), Xa-1 (Yoshimura et al. 1998, Expression of Xa-1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. PNAS, 95: 1663-1668) and Xa-26 (Sun et al. 2004, Xa26 a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an leucine-rich repeat LRR receptor kinase-like protein. Plant Journal, 37: 517-527), rice blast resistance gene Pi-b (Wang et al. 1999, The Pi-b gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant Journal, 1999, 19: 55-64) and Pi-ta (Bryan et al. 2000, A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell, 12: 2033-2046), and the tillering gene cloned by Li (Li et al. 2003, Control of tillering in rice. Nature 422: 618-621), salt tolerance gene (Ren et al. 2005, A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nature Genetics 37(10): 1141-1146) and high yield gene (Weiya Xue et al. 2008. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nature Genetics 40, 761-767).